Biology subjects

Simpson, A.

Publications and source records attributed to Simpson, A..

3 recordsLinked to original sources

bioRxiv2018

EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors, and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is a community driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the complete eukaryotic tree of life and microbial ecologists that actively use environmental sequencing data for the purpose of developing reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so.

microbiology↗

bioRxiv2017

Non-parametric mixture models identify trajectories of childhood immune development relevant to asthma and allergy

Events in early life contribute to subsequent risk of asthma; however, the causes and trajectories of childhood wheeze are heterogeneous and do not always result in asthma. Similarly, not all atopic individuals develop wheeze, and vice versa. The reasons for these differences are unclear. Using unsupervised model-based cluster analysis, we identified latent clusters within a prospective birth cohort with deep immunological and respiratory phenotyping. We characterised each cluster in terms of immunological profile and disease risk, and replicated our results in external cohorts from the UK and USA. We discovered three distinct trajectories, one of which is a high-risk \"atopic\" cluster with increased propensity for allergic diseases throughout childhood. Atopy contributes varyingly to later wheeze depending on cluster membership. Our findings demonstrate the utility of unsupervised analysis in elucidating heterogeneity in asthma pathogenesis and provide a foundation for improving management and prevention of childhood asthma.

systems biology↗

bioRxiv2017

Characterization Of NvLWamide-Like Neurons Reveals Stereotypy In Nematostella Nerve Net Development

Cnidarian nervous systems are traditionally described as diffuse nerve nets lacking true organization. However, there are examples of stereotypical structure in the nerve nets of multiple cnidarian species that suggest nerve nets are organized. We previously demonstrated that the NvashA target gene NvLWamide-like is expressed in a small subset of the Nematostella nerve net and speculated that observing a few neurons within the developing nerve net would provide a better indication of potential stereotypy. Here we document NvLWamide-like expression more systematically. NvLWamide-like is initially expressed in the typical neurogenic salt and pepper pattern within the ectoderm at the gastrula stage, and expression expands to include endodermal salt and pepper expression at the planula larval stage. Expression persists in both ectoderm and endoderm in adults. We generated an NvLWamide-like::mCherry transgenic reporter line to visualize the neural architecture. NvLWamide-like is expressed in six neural subtypes identifiable by neural morphology and location. Upon completing development the numbers of neurons in each neural subtype are minimally variable between animals and the projection patterns of each subtype are consistent. Between the juvenile polyp and adult stages the number of neurons for each subtype increases. We conclude that cnidarian nerve nets are organized, develop in a stereotyped fashion, and that one aspect of generating the adult nervous system is to modify the juvenile nervous system by increasing neural number proportionally with size.

developmental biology↗